Michał Burdukiewicz

• PhD
• Group Leader at Medical University of Białystok

Introduction Accurate post-mortem interval (PMI) estimation is essential in forensic investigations. Although various methods for PMI determination have been developed, only an approximate estimation is still achievable, and an accurate PMI indication is still challenging. Therefore, in this study, we employed gas chromatography-mass spectrometry (...

In biomedical literature, one of the most widely employed statistical procedures to analyze and visualize the association between two variables is linear regression. Data points that exert influence on the fit and its parameters are routinely, but not as often as required, identified by established influence measures and their corresponding cut-off...

Protein aggregation is responsible for several degenerative conditions in humans, and it is also a bottleneck in industrial protein production and storage of biotherapeutics. Bioinformatics tools have been developed to predict and redesign protein solubility more efficiently by understanding the underlying principles behind aggregation. As more exp...

Background Proteins self-organize in dynamic cellular environments by assembling into reversible biomolecular condensates through liquid-liquid phase separation (LLPS). These condensates can comprise single or multiple proteins, with different roles in the ensemble’s structural and functional integrity. Driver proteins form condensates autonomously...

Adhesins are crucial factors in the virulence of bacterial pathogens such as Escherichia coli. However, to date no resources have been dedicated to the detailed analysis of E. coli adhesins. Here, we provide adhesiomeR software that enables characterization of the complete adhesin repertoire, termed the adhesiome. AdhesiomeR incorporates the most c...

Peptides are attracting a growing interest as therapeutic agents. This trend stems from their cost‐effectiveness and reduced immunogenicity, compared to antibodies or recombinant proteins, but also from their ability to dock and interfere with large protein–protein interaction surfaces, and their higher specificity and better biocompatibility relat...

Protein aggregation is behind the genesis of incurable diseases and imposes constraints on drug discovery and the industrial production and formulation of proteins. Over the years, we have been advancing the Aggresscan3D (A3D) method, aiming to deepen our comprehension of protein aggregation and assist the engineering of protein solubility. Since i...

NanoString nCounter is a medium-throughput technology used in mRNA and miRNA differential expression studies. It offers several advantages, including the absence of an amplification step and the ability to analyze low-grade samples. Despite its considerable strengths, the popularity of the nCounter platform in experimental research stabilized in 20...

Motivation Missing values are commonly observed in metabolomics data from mass spectrometry. Imputing them is crucial because it assures data completeness, increases the statistical power of analyses, prevents inaccurate results, and improves the quality of exploratory analysis, statistical modeling, and machine learning. Numerous Missing Value Imp...

Parkinson’s disease (PD) is the second most prevalent neurodegenerative disorder, yet effective treatments able to stop or delay disease progression remain elusive. The aggregation of a presynaptic protein, α-synuclein (aSyn), is the primary neurological hallmark of PD and, thus, a promising target for therapeutic intervention. However, the lack of...

Protein aggregation has been associated with aging and different pathologies and represents a bottleneck in the industrial production of biotherapeutics. Numerous past studies performed in Escherichia coli and other model organisms have allowed to dissect the biophysical principles underlying this process. This knowledge fuelled the development of...

Due to their complex history, plastids possess proteins encoded in the nuclear and plastid genome. Moreover, these proteins localize to various subplastid compartments. Since protein localization is associated with its function, prediction of subplastid localization is one of the most important steps in plastid protein annotation, providing insight...

Enterohaemolysin (Ehx) and alpha-haemolysin are virulence-associated factors (VAFs) causing the haemolytic phenotype in Escherichia coli. It has been shown that chromosomally and plasmid-encoded alpha-haemolysin are characteristic of specific pathotypes, virulence-associated factors and hosts. However, the prevalence of alpha- and enterohaemolysin...

Amyloids and antimicrobial peptides (AMPs) have many similarities, e.g., both kill microorganisms by destroying their membranes, form aggregates, and modulate the innate immune system. Given these similarities and the fact that the antimicrobial properties of short amyloids have not yet been investigated, we chose a group of potentially antimicrobi...

Peptides are known to possess a plethora of beneficial properties and activities: antimicrobial, anticancer, anti-inflammatory or the ability to cross the blood-brain barrier are only a few examples of their functional diversity. For this reason, bioinformaticians are constantly developing and upgrading models to predict their activity in silico, g...

Information about the impact of interactions between amyloid proteins on their fibrillization propensity is scattered among many experimental articles and presented in unstructured form. We manually curated information located in almost 200 publications (selected out of 562 initially considered), obtaining details of 883 experimentally studied inte...

Antimicrobial peptides (AMPs) are a heterogeneous group of short polypeptides that target not only microorganisms but also viruses and cancer cells. Due to their lower selection for resistance compared with traditional antibiotics, AMPs have been attracting the ever-growing attention from researchers, including bioinformaticians. Machine learning r...

Antimicrobial peptides (AMPs) are a heterogeneous group of short polypeptides that target microorganisms but also viruses and cancer cells. Due to their lower selection for resistance compared to traditional antibiotics, AMPs have been attracting the ever-growing attention from researchers, including bioinformaticians. Machine learning represents t...

Human S100B is a small, multifunctional protein. Its activity, inside and outside cells, contributes to the biology of the brain, muscle, skin, and adipocyte tissues. Overexpression of S100B occurs in Down Syndrome, Alzheimer’s disease, Creutzfeldt–Jakob disease, schizophrenia, multiple sclerosis, brain tumors, epilepsy, melanoma, myocardial infarc...

The rapid influx of low-quality data visualizations is one of the main challenges in today’s commu- nication. Misleading, unreadable, or confusing visualizations spread misinformation. Furthermore, they fail to deliver their message to the viewer. The scale of the problem is big enough that there already exist public fora gathering tens of thousand...

Since the discovery of haemolysis, many studies focused on a deeper understanding of this phenotype in Escherichia coli and its association with other virulence genes, diseases and pathogenic attributes/functions in the host. Our virulence-associated factor profiling and genome-wide association analysis of genomes of haemolytic and nonhaemolytic E....

Amyloid proteins (amyloids) have a unique ability to assemble into filamentous aggregates characterized by the presence of cross-beta sheets. The aggregation of amyloid fibrils is associated with the pathology seen in a wide range of diseases known as amyloidosis. This process can be accelerated or slowed by already formed amyloid fibrils constitut...

Cross seeding between amyloidogenic proteins in the gut is receiving increasing attention as a possible mechanism for initiation or acceleration of amyloid formation by aggregation‐prone proteins such as αSN, which is central in the development of Parkinson's disease (PD). This is particularly pertinent in view of the growing number of functional (...

CsgA is an aggregating protein from bacterial biofilms, representing a class of functional amyloids. Its amyloid propensity is defined by five fragments (R1–R5) of the sequence, representing non-perfect repeats. Gate-keeper amino acid residues, specific to each fragment, define the fragment’s propensity for self-aggregation and aggregating characte...

Several disorders are related to amyloid aggregation of proteins, for example Alzheimer’s or Parkinson’s diseases. Amyloid proteins form fibrils of aggregated beta structures. This is preceded by formation of oligomers—the most cytotoxic species. Determining amyloidogenicity is tedious and costly. The most reliable identification of amyloids is obt...

Cross-seeding between amyloidogenic proteins in the gut is receiving increasing attention as a possible mechanism for initiation or acceleration of amyloid formation by aggregation-prone proteins such as αSN, which is central in the development of Parkinson’s disease. This is particularly pertinent in view of the growing number of functional ( i.e....

Motivation: Quantitative Real-time PCR (qPCR) is a widely used -omics method for the precise quantification of nucleic acids, in which the result is associated with the presence/absence or quantity of a specific nucleic acid sequence. As the amount of qPCR data increases worldwide, the manual assessment of results becomes challenging and difficult...

Background: DNA double-strand breaks can be counted as discrete foci by imaging techniques. In personalized medicine and pharmacology, the analysis of counting data is relevant for numerous applications, e.g., for cancer and aging research and the evaluation of drug efficacy. By default, it is assumed to follow the Poisson distribution. This assum...

The study of microbiomes has gained in importance over the past few years and has led to the emergence of the fields of metagenomics, metatranscriptomics, and metaproteomics. While initially focused on the study of biodiversity within these communities, the emphasis has increasingly shifted to the study of (changes in) the complete set of functions...

Salmonella is a foodborne pathogen affecting over 200 million people and resulting in over 200,000 fatal cases per year. Its adhesion to and invasion into intestinal epithelial cells represent one of the first and key steps in the pathogenesis of salmonellosis. Still, around 35 to 40% of bacterial genes have no experimentally validated function, an...

Reports on phase separation and amyloid formation for multiple proteins and aggregation-prone peptides are recurrently used to explore the molecular mechanisms associated with several human diseases. The information conveyed by these reports can be used directly in translational investigation, e.g., for the design of better drug screening strategie...

The study of microbiomes has gained in importance over the past few years, and has led to the fields of metagenomics, metatranscriptomics and metaproteomics. While initially focused on the study of biodiversity within these communities the emphasis has increasingly shifted to the study of (changes in) the complete set of functions available in thes...

Antimicrobial peptides (AMPs) constitute a diverse group of bioactive molecules that provide multicellular organisms with protection against microorganisms, and microorganisms with weaponry for competition. Some AMPs can target cancer cells; thus, they are called anticancer peptides (ACPs). Due to their small size, positive charge, hydrophobicity a...

Motivation: Hydrogen-deuterium mass spectrometry (HDX-MS) is a rapidly developing technique for monitoring dynamics and interactions of proteins. The development of new devices has to be followed with new software suites adressing emerging standards in data analysis. Results: We propose HaDeX, a novel tool for processing, analysis and vizualisation...

Antimicrobial peptides (AMPs) are molecules widespread in all branches of the tree of life that participate in host defense and/or microbial competition. Due to their positive charge, hydrophobicity and amphipathicity, they preferentially disrupt negatively charged bacterial membranes. AMPs are considered an important alternative to traditional ant...

The ratio between living and dead cells is an important parameter in microalgae culture and environmental monitoring. Fast, robust and automated analytical methods for monitoring microalgae growth for biotechnological and pharmaceutical applications and for optimizing production strains are needed. We developed a pipeline for the automatic binary c...

The rapid and simultaneous detection of DNA and protein biomarkers is necessary to detect the outbreak of a disease or to monitor a disease. For example, cardiovascular diseases are a major cause of adult mortality worldwide. We have developed a rapidly adaptable platform to assess biomarkers using a microfluidic technology. Our model mimics autoan...

We evaluated prevalence and distribution of antibiotic resistant E. coli in three categories: animals (goats, pigs, poultry, cattle, sheep), humans (butchers, meat sellers, animal farm workers, buyers) and animal food products (milk, cheese, beef, chicken, yoghurt) from selected animal farms in South-West Nigeria. The biofilm formation, phylogroupi...

Signal peptides are N-terminal presequences responsible for targeting proteins to the endomembrane system, and subsequent subcellular or extracellular compartments, and consequently condition their proper function. The significance of signal peptides stimulates development of new computational methods for their detection. These methods employ learn...

Amplification curves from quantitative Real-Time PCR experiments typically exhibit a sigmoidal shape. They can roughly be divided into a ground or baseline phase, an exponential amplification phase, a linear phase and finally a plateau phase, where in the latter, the PCR product concentration no longer increases. Nevertheless, in some cases the pla...

Bacterial host tropism is a primary determinant of the range of host organisms they can infect. Salmonella serotypes are differentiated into host-restricted and host-adapted specialists, and host-unrestricted generalists. In order to elucidate the underlying molecular mechanisms of host specificity in Salmonella infection, we investigated the role...

Sex determination in mammals is strongly linked to sex chromosomes. In most cases, females possess two copies of X chromosome while males have one X and one Y chromosome. It is assumed that these chromosomes originated from a pair of homologous autosomes, which diverged when recombination between them was suppressed. However, it is still debated wh...

The vast biodiversity of the microbial world and how little is known about it, has already been revealed by extensive metagenomics analyses. Our rudimentary knowledge of microbes stems from difficulties concerning their isolation and culture in laboratory conditions, which is necessary for describing their phenotype, among other things, for biotech...

Bacterial biofilm formation is a widespread phenomenon and a complex process requiring a set of genes facilitating the initial adhesion, maturation, and production of the extracellular polymeric matrix and subsequent dispersal of bacteria. Most studies on Escherichia coli biofilm formation have investigated nonpathogenic E. coli K-12 strains. Due t...

Amyloids are proteins associated with several clinical disorders, including Alzheimer’s, and Creutzfeldt-Jakob’s. Despite their diversity, all amyloid proteins can undergo aggregation initiated by short segments called hot spots. To find the patterns defining the hot spots, we trained predictors of amyloidogenicity, using n-grams and random forest...

Motivation: Reproducibility, a cornerstone of research, requires defined data formats, which include the set-up and output of experiments. The Real-time PCR Data Markup Language (RDML) is a recommended standard of the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines. Despite the popularity of the RDML...

Real-time quantitative polymerase chain reaction (qPCR) data are found to display periodic patterns in the fluorescence intensity as a function of sample number for fixed cycle number. This behavior is seen for technical replicate datasets recorded on several different commercial instruments; it occurs in the baseline region and typically increases...

The estimated mean copy per partition (λ) is the essential information from a digital PCR (dPCR) experiment because λ can be used to calculate the target concentration in a sample. However, little information is available how to statistically compare dPCR runs of multiple runs or reduplicates. The comparison of λ values from several runs is a multi...

Amyloids are proteins associated with the number of clinical disorders (e.g., Alzheimer's, Creutzfeldt-Jakob's and Huntington's diseases). Despite their diversity, all amyloid proteins can undergo aggregation initiated by 6- to 15-residue segments, called hot spots. To find the patterns defining the hot-spots, we trained predictors of amyloidogenic...

Amyloids are proteins associated with the number of clinical disorders (e.g., Alzheimer's, Creutzfeldt-Jakob's and Huntington's diseases). Despite their diversity, all amyloid proteins can undergo aggregation initiated by 6- to 15-residue segments, called hot spots. To find the patterns defining the hot-spots, we trained predictors of amyloidogenic...

The confidence intervals of the results of the experiment. Each chart consists of p-values (represented by dots) of MRT performed on runs from two different relative concentrations. For example, top left chart contains p-values of tests comparing runs with 100% and 0% of relative template concentration. The red line denotes confidence level 0.05.

Monte Carlo evaluation of the GLM and MRT methods for number of runs in a single group from one to four. Columns describe respectively: number of runs in the single group in the comparison, the λ value in group 1, the λ value in group 2, average p-value computed using GLM, average p-value computed using MRT.

The impact of number of runs on the average time of data analysis by GLM and MRT methods. Columns describe: number of runs in the single group in the comparison, number of partitions in the single run, mean time of data analysis by GLM (in seconds), mean time of data analysis by MRT (in seconds).

The confidence intervals of the experiment results. Columns describe: dilution of sample, method of computing CIs, λ value, lower border of CI, upper border of CI, assumed λ value.

The code used to perform analysis of the experimental data.

Monte Carlo evaluation of the GLM and MRT methods for number of runs in a single group from one to four. The colour of the tile describes the range to which p-value belongs (0–0.001, 0.001–0.05, 0.05–1). Two first ranges indicate significant results. The number inside each cell is the exact p-value.

Probability of λ coverage based on confidence intervals calculated by adjusted Dunn–Šidák correction in comparison to Bhat's and Dube's methods. Columns describe respectively: λ value, type of the probability coverage, confidence intervals provided by MRT method, confidence intervals provided by Bhat's method, confidence intervals provided by Dube'...

The table contains the p-values of the experiment results. Columns describe: dilution of sample 1, dilution of sample 2, p-value computed by MRT.

Absolute Quantification of Nucleic Acids on a Planar Droplet Digital PCR Array

There is an ever-increasing number of applications, which use quantitative PCR (qPCR) or digital PCR (dPCR) to elicit fundamentals of biological processes. Moreover, quantitative isothermal amplification (qIA) methods have become more prominent in life sciences and point-of-care- diagnostics. Additionally, the analysis of melting data is essential...

(qPCR) and quantitative isothermal amplification (qIA) are standard methods for nucleic acid quantification. Numerous real-time read-out technologies have been developed. Despite the continuous interest in amplification-based techniques, there are only few tools for pre-processing of amplification data. However, a transparent tool for precise contr...

Escherichia coli bacteria are the most common causes of diarrhea and septicemia in calves. Moreover, calves form a major reservoir for transmission of pathogenic E. coli to humans. Systematic reviews and meta-analyses of publications on E. coli as calf pathogens and the role of calves as reservoir have not been done so far. We reviewed studies betw...

Background: Quantification cycle (Cq) and amplification efficiency (AE) are parameters mathematically extracted from raw data to characterize quantitative PCR (qPCR) reactions and quantify the copy number in a sample. Little attention has been paid to the effects of preprocessing and the use of smoothing or filtering approaches to compensate for n...